Variant report

Variant	rs9400677
Chromosome Location	chr6:114185499-114185500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:114184976..114187157-chr6:114188705..114190881,2	MCF-7	breast:
2	chr6:114183529..114185723-chr6:114208542..114210250,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11153451	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146178	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348779	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945978	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945980	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs638614	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920267	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6934011	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7771208	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs922329	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372383	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9384885	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9387181	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9400679	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9488271	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs975257	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9400677	LOC285758	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114181000-114200200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:114181200-114193200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:114181800-114186000	Weak transcription	Lung	lung
4	chr6:114181800-114193200	Weak transcription	Liver	Liver
5	chr6:114181800-114194200	Weak transcription	Pancreas	Pancrea
6	chr6:114182000-114187400	Weak transcription	Colonic Mucosa	Colon
7	chr6:114182200-114192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:114182200-114194200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:114182200-114194200	Weak transcription	Ovary	ovary
10	chr6:114182400-114193000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:114182400-114193200	Weak transcription	Fetal Intestine Large	intestine
12	chr6:114182600-114193000	Weak transcription	HepG2	liver
13	chr6:114182800-114193000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:114183000-114185800	Weak transcription	Fetal Stomach	stomach
15	chr6:114183200-114196200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:114183600-114185600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:114183600-114196400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:114183800-114186200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:114183800-114193400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:114183800-114196200	Weak transcription	NHLF	lung
21	chr6:114183800-114200200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:114183800-114200400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:114184000-114186000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:114184000-114186000	Weak transcription	Placenta	Placenta
25	chr6:114184000-114186600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:114184000-114191000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:114184000-114193200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:114184000-114193200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:114184000-114194200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:114184000-114200200	Weak transcription	Fetal Kidney	kidney
31	chr6:114184200-114187200	Weak transcription	Fetal Brain Male	brain
32	chr6:114184200-114193000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:114184200-114193200	Weak transcription	Primary B cells from cord blood	blood
34	chr6:114184200-114194200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:114184200-114194200	Weak transcription	HUVEC	blood vessel
36	chr6:114184200-114195800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:114184200-114196000	Weak transcription	HSMM	muscle
38	chr6:114184200-114196400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:114184400-114187800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:114184400-114188000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:114184400-114188400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:114184400-114191600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:114184400-114192400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:114184400-114194200	Weak transcription	Fetal Lung	lung
45	chr6:114184400-114194200	Weak transcription	Fetal Thymus	thymus
46	chr6:114184400-114196200	Weak transcription	NH-A	brain
47	chr6:114184600-114186800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:114184600-114193000	Weak transcription	NHDF-Ad	bronchial
49	chr6:114184800-114193200	Weak transcription	Osteobl	bone
50	chr6:114185400-114185600	Enhancers	Colon Smooth Muscle	Colon

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